The first time a window appears there is a "gap" near the top of the screen, a space where you can see through to the background (or whatever window is underneath). It's really hard to explain, so here's a picture instead:
As you can see in the picture above, there's this... gap at the top of the window. (I'm using maximus to have windows always be maximized and to hide window decorations.)
If you switch to a different window and then back again, the gap goes away.
If you minimize and restore the window, the gap goes away.
When the "gap" is there, clicking on anything in the window reveals that what you see isn't what you're clicking on. That is, the window behaves as if the gap wasn't there. The best way I can describe this is that it's almost like the window is vertically offset by the same amount as the height of the gap at the top.
For example: In the picture above, if I tried to click on the "keith" folder in the places column on the left, it would end up clicking on "Desktop" instead - as if the whole window is offset by a little bit.
What could be causing this?